Genomic innovation- Paralogy Cotton, Methods in Enzymology, 2005
Homology, Orthology, Paralogy Homology is a relation between a pair of genes that share a common ancestor. Orthology is a relation defined over a pair of homologous genes, where the two genes have emerged through a speciation event Paralogy is a relation defined over a pair of homologous genes that have emerged through a gene duplication A.M. Altenhoff and C. Dessimoz, Inferring Orthology and Paralogy
In and out Paralogy In-paralogy if they are paralogs and duplicated after the speciation event of reference Out-paralogy if the duplication event through which they are related to each other predates the speciation event of reference
Ensembl A joint project between EMBL - European Bioinformatics Institute (EBI) and the Wellcome Trust Sanger Institute (WTSI) A genome browser for the retrieval of genomic information http://www.ensembl.org
BioMart BioMart is a search engine that can find multiple terms and put them into a table format. Such as: human gene (IDs), chromosome and base pair position
1)Choose the species of interest (Dataset) 2)Decide what you would like to know about the genes (Attributes) (sequences, IDs, description…) 1)Decide on a smaller geneset using Filters. (enter IDs, choose a region …) How does BioMart work?
Choose the species of interest Choose the gene set Choose the information you want to view BioMart
Choose the species of interest: Homo sapiens is the default BioMart
Sequences: UTRs, flanking sequences, cDNA and peptides, etc Gene IDs from Ensembl and external sources (MGI, Entrez, etc.) Microarray data Protein Functions/descriptions (Interpro, GO) Orthologous gene sets SNP/ Variation Data What else can we do with BioMart?